There is no way for PyAI to tell which order you want to decompile your scripts, it decompiles them in the order they are referenced by the script that jumps to them (not in the order they were compiled). You could just export/import the script to a text file to keep the order/labels/comments.

Hmm I don't know how that could have got through all this time. Well the only way for it to be fixed at the moment is to use the source version and the patch I've listed bellow. If you aren't using the source version already download it here as well as Python (preferably 2.5.4 from here).

Next open up PyMSLibsAIBIN.py and edit line 396, which should look like this (bold line):